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BAM_TALLY_FILES = fopen.h bool.h types.h bam.h bgzf.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
interval.c interval.h uintlist.c uintlist.h \
stopwatch.c stopwatch.h access.c access.h iitdef.h iit-read.c iit-read.h \
chrom.c chrom.h genomicpos.c genomicpos.h \
md5.c md5.h complement.h sequence.c sequence.h genome.c genome.h \
uinttable.c uinttable.h table.c table.h \
chrnum.c chrnum.h \
samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \
matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \
translation.c translation.h expr.c expr.h bamtally.c bamtally.h \
datadir.c datadir.h \
getline.c getline.h getopt.c getopt1.c getopt.h bamtally_main.c
@HAVE_SAMTOOLS_LIB_TRUE@bam_tally_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_CFLAGS) $(POPCNT_FLAGS) $(SAMTOOLS_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
@HAVE_SAMTOOLS_LIB_TRUE@bam_tally_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS) $(SAMTOOLS_LDFLAGS)
@HAVE_SAMTOOLS_LIB_TRUE@bam_tally_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(SAMTOOLS_LIBS)
@HAVE_SAMTOOLS_LIB_TRUE@dist_bam_tally_SOURCES = $(BAM_TALLY_FILES)
LIBGSTRUCT_LA_FILES = config.h fopen.h bool.h types.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
interval.c interval.h uintlist.c uintlist.h \
stopwatch.c stopwatch.h access.c access.h iitdef.h iit-read.c iit-read.h \
complement.h chrom.c chrom.h genomicpos.c genomicpos.h \
md5.c md5.h sequence.c sequence.h genome.c genome.h \
uinttable.c uinttable.h table.c table.h \
chrnum.c chrnum.h \
samflags.h bamread.c bamread.h samread.c samread.h parserange.c parserange.h \
tableuint.c tableuint.h iit-write.c iit-write.h ucharlist.c ucharlist.h \
matchdef.h matchpool.c matchpool.h mismatchdef.h mismatchpool.c mismatchpool.h tally.c tally.h \
translation.c translation.h expr.c expr.h bamtally.c bamtally.h \
datadir.c datadir.h
# Do not add SAMTOOLS LIBS here
@HAVE_SAMTOOLS_LIB_TRUE@libgstruct_@LIBGSTRUCT_API_VERSION@_la_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(SIMD_CFLAGS) $(POPCNT_FLAGS) $(SAMTOOLS_CFLAGS) -fPIC -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
@HAVE_SAMTOOLS_LIB_TRUE@libgstruct_@LIBGSTRUCT_API_VERSION@_la_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS) -version-info $(LIBGSTRUCT_SO_VERSION)
@HAVE_SAMTOOLS_LIB_TRUE@libgstruct_@LIBGSTRUCT_API_VERSION@_la_LIBADD = $(PTHREAD_LIBS) $(ZLIB_LIBS)
@HAVE_SAMTOOLS_LIB_TRUE@dist_libgstruct_@LIBGSTRUCT_API_VERSION@_la_SOURCES = $(LIBGSTRUCT_LA_FILES)
#gstruct_includedir = $(includedir)/gstruct-$(LIBGSTRUCT_API_VERSION)
#gstruct_include_HEADERS = bamtally.h
gstruct_includedir = $(includedir)
gstruct_include_HEADERS = config.h fopen.h bool.h types.h \
except.h assert.h mem.h \
intlistdef.h intlist.h listdef.h list.h \
littleendian.h bigendian.h \
interval.h uintlist.h \
stopwatch.h access.h iitdef.h iit-read.h \
chrom.h genomicpos.h \
md5.h complement.h sequence.h genome.h \
uinttable.h table.h \
chrnum.h \
bamread.h samread.h parserange.h \
dynprog.h dynprog_nogap.h dynprog_simd.h dynprog_cigar.h dynprog_single.h \
tableuint.h iit-write.h ucharlist.h \
matchdef.h matchpool.h mismatchdef.h mismatchpool.h tally.h translation.h bamtally.h datadir.h
# May want nodist_bamtally_libinclude_HEADERS = ../lib/bamtally.h
#bamtally_libincludedir = $(libdir)/bamtally-$(LIBGSTRUCT_API_VERSION)/include
#nodist_bamtally_libinclude_HEADERS = bamtally-config.h
pkgconfigdir = $(libdir)/pkgconfig
pkgconfig_DATA = ../lib/gstruct-$(LIBGSTRUCT_API_VERSION).pc
all: config.h
$(MAKE) $(AM_MAKEFLAGS) all-am
.SUFFIXES:
.SUFFIXES: .c .lo .o .obj
$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__configure_deps)
@for dep in $?; do \
case '$(am__configure_deps)' in \
*$$dep*) \
( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
&& { if test -f $@; then exit 0; else break; fi; }; \
exit 1;; \
esac; \
done; \
echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
$(am__cd) $(top_srcdir) && \
$(AUTOMAKE) --gnu src/Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
*config.status*) \
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
*) \
echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
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$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(am__aclocal_m4_deps):
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@test -f $@ || $(MAKE) $(AM_MAKEFLAGS) stamp-h1
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@rm -f stamp-h1
cd $(top_builddir) && $(SHELL) ./config.status src/config.h
$(srcdir)/config.h.in: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
($(am__cd) $(top_srcdir) && $(AUTOHEADER))
rm -f stamp-h1
touch $@
distclean-hdr:
-rm -f config.h stamp-h1
install-libLTLIBRARIES: $(lib_LTLIBRARIES)
@$(NORMAL_INSTALL)
@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
list2=; for p in $$list; do \
if test -f $$p; then \
list2="$$list2 $$p"; \
else :; fi; \
done; \
test -z "$$list2" || { \
echo " $(MKDIR_P) '$(DESTDIR)$(libdir)'"; \
$(MKDIR_P) "$(DESTDIR)$(libdir)" || exit 1; \
echo " $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 '$(DESTDIR)$(libdir)'"; \
$(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL) $(INSTALL_STRIP_FLAG) $$list2 "$(DESTDIR)$(libdir)"; \
}
uninstall-libLTLIBRARIES:
@$(NORMAL_UNINSTALL)
@list='$(lib_LTLIBRARIES)'; test -n "$(libdir)" || list=; \
for p in $$list; do \
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$(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=uninstall rm -f "$(DESTDIR)$(libdir)/$$f"; \
done
clean-libLTLIBRARIES:
-test -z "$(lib_LTLIBRARIES)" || rm -f $(lib_LTLIBRARIES)
@list='$(lib_LTLIBRARIES)'; \
locs=`for p in $$list; do echo $$p; done | \
sed 's|^[^/]*$$|.|; s|/[^/]*$$||; s|$$|/so_locations|' | \
sort -u`; \
test -z "$$locs" || { \
echo rm -f $${locs}; \
rm -f $${locs}; \
}
libgstruct-@LIBGSTRUCT_API_VERSION@.la: $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_OBJECTS) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_DEPENDENCIES) $(EXTRA_libgstruct_@LIBGSTRUCT_API_VERSION@_la_DEPENDENCIES)
$(AM_V_CCLD)$(libgstruct_@LIBGSTRUCT_API_VERSION@_la_LINK) -rpath $(libdir) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_OBJECTS) $(libgstruct_@LIBGSTRUCT_API_VERSION@_la_LIBADD) $(LIBS)
install-binPROGRAMS: $(bin_PROGRAMS)
@$(NORMAL_INSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
if test -n "$$list"; then \
echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
$(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
fi; \
for p in $$list; do echo "$$p $$p"; done | \
sed 's/$(EXEEXT)$$//' | \
while read p p1; do if test -f $$p \
|| test -f $$p1 \
; then echo "$$p"; echo "$$p"; else :; fi; \
done | \
sed -e 'p;s,.*/,,;n;h' \
-e 's|.*|.|' \
-e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
sed 'N;N;N;s,\n, ,g' | \
$(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
{ d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
if ($$2 == $$4) files[d] = files[d] " " $$1; \
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END { for (d in files) print "f", d, files[d] }' | \
while read type dir files; do \
if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
test -z "$$files" || { \
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$(INSTALL_PROGRAM_ENV) $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=install $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
} \
; done
uninstall-binPROGRAMS:
@$(NORMAL_UNINSTALL)
@list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
-e 's/$$/$(EXEEXT)/' \
`; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(bindir)" && rm -f $$files
clean-binPROGRAMS:
@list='$(bin_PROGRAMS)'; test -n "$$list" || exit 0; \
echo " rm -f" $$list; \
rm -f $$list || exit $$?; \
test -n "$(EXEEXT)" || exit 0; \
list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
echo " rm -f" $$list; \
rm -f $$list
bam_tally$(EXEEXT): $(bam_tally_OBJECTS) $(bam_tally_DEPENDENCIES) $(EXTRA_bam_tally_DEPENDENCIES)
@rm -f bam_tally$(EXEEXT)
$(AM_V_CCLD)$(bam_tally_LINK) $(bam_tally_OBJECTS) $(bam_tally_LDADD) $(LIBS)
mostlyclean-compile:
-rm -f *.$(OBJEXT)
distclean-compile:
-rm -f *.tab.c
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-access.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-assert.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-bamread.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-bamtally.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-bamtally_main.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-bigendian.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-chrnum.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-chrom.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-datadir.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-except.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-expr.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-genome.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-genomicpos.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-getline.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-getopt.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-getopt1.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-iit-read.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-iit-write.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-interval.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-intlist.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-list.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-littleendian.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-matchpool.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-md5.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-mem.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-mismatchpool.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-parserange.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-samread.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-sequence.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-stopwatch.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-table.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-tableuint.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-tally.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-translation.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-ucharlist.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-uintlist.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/bam_tally-uinttable.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-access.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-assert.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamread.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-bamtally.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-bigendian.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-chrnum.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-chrom.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-datadir.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-except.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-expr.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-genome.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-genomicpos.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-iit-read.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-iit-write.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-interval.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-intlist.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-list.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-littleendian.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-matchpool.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-md5.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-mem.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-mismatchpool.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-parserange.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-samread.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-sequence.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-stopwatch.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-table.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-tableuint.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-tally.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-translation.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-ucharlist.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-uintlist.Plo@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/libgstruct_@LIBGSTRUCT_API_VERSION@_la-uinttable.Plo@am__quote@
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